What can I check beside leaks,spark plugs,coils and connectors on 1999 Ford Expedition

Checked with a Valve Guage Tester and read Late Ingition Timing
I have checked for leaks
Coil on plugs good
Put new spark plugs

Asked by for the 1999 Ford Expedition
What are you checking for, tell us what the problem is!
Did a tune up.
Started to run with a rough idle and smoking
Was not doing this before tune up
Rechecked everything to make sure
So checked with a gauge and it read LATE INGITION TIMING
Also no codes have come out
So trying to find out what has caused this
It also wants to stall
try dis connect battery for a few minutes. comp. should go to default. might help.